rigid bodies violently jumping away
The problem is that this simulation is to perform in an automated process where human-designed but random assemblies are put through a physics simulation, so it's impossible to fit the correct collision shapes by hand. Fortunately, I have made some progress. The (at least partial) solution was to do a convex decomposition of the mesh, after chopping the entire thing up into manageable blocks.The whole process is this:

split the mesh into its components (mechanical separate parts)
subdivide those components into 3x3x3 blocks
split those blocks up into isolated parts
perform an approximate convex decomposition on those parts.
finally, assemble all the convex hulls into groups that approximate the original components

Although it requires a lot of processing, the results are quite stunning. You can now interactively manipulate one of the more complex assemblies in the set. I haven't tested this on other production models yet, but at least there is some real improvement in the quality of the simulation.